<p>Postoperative patients with complex congenital heart disease (CHD), such as those who have undergone Fontan procedures or Tetralogy of Fallot (TOF) repairs, often experience complications, including arrhythmias and heart failure. Heart rate variability (HRV) analysis assesses autonomic function and predicts cardiac outcomes; however, conventional linear methods have limitations, particularly in pediatric populations with variable heart rates. Nonlinear HRV analysis offers a robust alternative. This study evaluated the utility of nonlinear HRV indices to identify early autonomic dysfunction in postoperative patients with CHD. A total of 41 postoperative patients with CHD (22 Fontan, 19 TOF) and 34 age-matched healthy controls underwent 24-h electrocardiogram recordings during sleep. Frequency- and time-domain HRV indices were calculated, alongside nonlinear measures such as Poincaré plot analysis and Higuchi fractal dimension (HFD). Statistical analyses compared the groups and assessed correlations between HRV indices and clinical parameters. Patients who underwent TOF repairs exhibited significantly lower low frequency, high frequency, standard deviation of all normal R-R intervals, and the root mean square of successive differences between R-R intervals values than those in the control group. Nonlinear indices, particularly HFD, were unaffected by heart rate, enhancing reliability in pediatric populations. Age-related declines in fractal indices in postoperative patients with TOF repairs suggest progressive autonomic dysfunction. Nonlinear HRV analysis offers valuable insights into autonomic dysregulation in postoperative patients with CHD, surpassing conventional methods in reliability. These approaches may enable early detection of autonomic deterioration, improving risk stratification and guiding management. Further validation in larger cohorts is warranted.</p>